Recent Publications

The most updated list of publications by the Northen Lab is available via google scholar


Sordo, Z., Andeer, P., Sethian, J., Northen, T., Ushizima, D. (2024) RhizoNet segments plant roots to assess biomass and growth for enabling self-driving labs. Sci Rep 14, 12907.

Liu, Y., Zhao, X., Gan, F., Chen. X., Deng, K., Crowe, S. A., Hudson, G. A., Belcher, M. S., Schmidt, M., Astolfi, M. C. T., Kosina, S., Pang, B., Shao, M., Yin, J., Sirirungruang, S., Iavarone, A., T., Reed, J., Martin, L. B. B., El-Demerdash, A., Kikuchi, S., Misra, R. C., Liang, X., Cronce, M. J., Chen, X., Zhan, C., Kakumanu, R., Baidoo, E., E. K., Chen, Y., Petzold, C. J., Northen, T. R., Osbourn, A., Scheller, H., Keasling, J. D. (2024) Complete biosynthesis of QS-21 in engineered yeast. Nature 629, 937–944.

Markel, K., Novak, V., Bowen, B. P., Tian, Y., Chen, Y., Sirirungruang, S., Zhou, A., Louie, K. B., Northen, T. R., Eudes, A., Scheller, H. V., Shih, P. M. Cynipid wasps systematically reprogram host metabolism and restructure cell walls in developing galls, Plant Physiology, Volume 195, Issue 1, May 2024, Pages 698–712,

Schadt, C., Martin, S., Carrell, A., Fortner, A., Hopp, D., Jacobson, D., Klingeman, D., Kristy, B., Phillips, J., Piatkowski, B., Miller, M. A., Smith, M., Patil, S., Flynn, M., Canon, S., Clum, A., Mungall, C. J., Pennacchio, C., Bowen, B., Louie, K., Northen, T., Elow-Fadrosh, E. A., Mayes, M. A., Muchero, W., Weston, D. J., Mitchell, J., Doktycz, M. (2024) An integrated metagenomic, metabolomic and transcriptomic survey of Populus across genotypes and environments. Sci Data 11, 339.

Song, Y., Yao, S., Li, X., Wang, T., Jiang, X., Bolan, N., Warren, C. R., Northen, T. R., Chang, S. X. (2024) Soil metabolomics: Deciphering underground metabolic webs in terrestrial ecosystems. ScienceDirect.

Lin, H. H., Torres, M., Adams, C. A., Andeer, P. F., Owens, T. K., Zhalnina, K., Jabusch, L.K., Carlson, H. K., Kuehl, J. V., Deutschbauer, A. M., Northen, T. R., Glass, N. L., Mortimer, J. C. (2024) Impact of Inoculation Practices on Microbiota Assembly and Community Stability in a Fabricated Ecosystem. APS Publications.

Pham, L.T.M.; Deng, K.; Choudhary, H.; Northen, T.R.; Singer, S.W.; Adams, P.D.; Simmons, B.A.; Sale, K.L. (2024) An Engineered Laccase from Fomitiporia mediterranea Accelerates Lignocellulose Degradation. Biomolecules. 14, 324.

Feitosa-Junior, O.R., Lubbe, A., Kosina, S. M., Martins-Junior, J., Barbosa, D., Baccari, C., Zaini, P. A., Bowen, B. P., Northen, T. R., Lindow, S. E., et al. (2024) The Exometabolome of Xylella fastidiosa in Contact with Paraburkholderia phytofirmans Supernatant Reveals Changes in Nicotinamide, Amino Acids, Biotin, and Plant Hormones. Metabolites, 14, 82.

Novak, V., Andeer, P. F., Bowen, B. P., Ding, Y., Zhalnina, K., Tomaka, C., Golini, A. N., Kosina, S. M., Northen, T. R. (2024) Reproducible growth of Brachypodium in EcoFAB 2.0 reveals that nitrogen form and starvation modulate root exudation. Science Advances 10,1.


Caddell, D., Pettinga, D., Louie, K., Bowen, B., Sievert, J. A., Hollingsworth, J., Rubanowitz, R., Dahlberg, J., Purdom, E., Northen, T., Coleman-Derr, D. (2023) Drought shifts sorghum root metabolite and microbiome profiles and enriches for pipecolic acid. Phytobiomes Journal. 

Yi, X., Rasor, B. J., Boadi, N., Louie, K., Northen, T. R., Sarim, A. S., Jewett, M. C., Alper, S. A. (2023) Establishing a versatile toolkit of flux enhanced strains and cell extracts for pathway prototyping. Metabolic Engineering.

Zheng, Q., Hu, Y., Kosina, S. M., Van Goethem, M. W., Tringe, S. G., Bowen, B. P., Northen, T. R. (2023) Conservation of beneficial microbes between the rhizosphere and the cyanosphere. New Phytologist. 240: 1246–1258.

Džunková, M., La Clair, J.J., Tyml, T., Doud, D., Schulz, F., Piquer-Esteban, S., Sanchis, D. P., Osborn, A., Robinson, D., Louie, K. B., Bowen, B. P., Bowers, R. M., Lee, J., Arnau, V., Diaz, Villanueva, W., Stepanauskas, R., Gosliner, T., Northen, T. R., Cheng, J. F., Burkart, M. D., Woyke, T. (2023) Synthase-selected sorting approach identifies a beta-lactone synthase in a nudibranch symbiotic bacterium. Microbiome 11, 130.

Strenkert, D., Schmollinger, S., Hu, Y., Hofmann, C., Holbrook, K., Liu, H. W., Purvine, S. O., Nicora, C. D., Chen, S., Lipton, M. S., Northen, T. R., Clemens, S. Merchant, S. S. (2023) Zn deficiency disrupts Cu and S homeostasis in Chlamydomonas resulting in over accumulation of Cu and Cysteine.

Chen, Y., Gin, J. W., Wang, Y., de Raad, M., Tan, S., Hillson, N. J., Northen, T. R., Adams, P. D., Petzold, C. J. (2023) Alkaline-SDS cell lysis of microbes with acetone protein precipitation for proteomic sample preparation in 96-well plate format. PLoS ONE 18(7): e0288102.

Takasuka, T., Kim, H., Deng, K., Bianchetti, C. M., Yamashita, K., Beebe, E. T., Bergeman, L. F., Meulen, K. A. V., Deutsch, S., Ralph. J., Adams, P. D., Northen, T. R., Fox, B. G. (2023) Quantitative Analysis of the High Yield Hydrolysis of Kelp by Laminarinase and Alginate Lyase. ChemBioChem.

Davenport, R., Bowen, B. P., Lynch, L. M., Kosina, S. M., Shabtai, I., Northen, T. R., Lehmann, J. (2023). Decomposition decreases molecular diversity and ecosystem similarity of soil organic matter. In Proceedings of the National Academy of Sciences (Vol. 120, Issue 25). Proceedings of the National Academy of Sciences.

Brisson, V., Swink, C., Kimbrel, J., Mayali, X., Samo, T., Kosina, S. M., Thelen, M., Northen, T. R., Stuart, R. K. (2023) Dynamic Phaeodactylum tricornutum exometabolites shape surrounding bacterial communities. New Phytologist.

Acharya, S.M., Yee, M.O., Diamond, S., Andeer, P. F., Baig, N. F., Aladesanmi, O.T., Northen, T. R., Banfield, J. F., Chakraborty, R. (2023) Fine scale sampling reveals early differentiation of rhizosphere microbiome from bulk soil in young Brachypodium plant roots. ISME COMMUN. 3, 54.

Huang J., Quest, A., Cruz-Morales, P., Deng, K., Pereira, J. H., Van Cura, D., Kakumanu, R., Baidoo, E. E. K, Dan, Q., Chen, Y., Petzold, C. J., Northen, T. R., Adams, P. D., Clark. D. S., Balskus, E. P., Hartwig, J. F., Mukhopadhyay, A., Keasling, J. D. (2023)  Complete integration of carbene-transfer chemistry into biosynthesis. Nature 617, 403–408.

Englund, E., Schmidt, M., Nava, A. A., Lechner, A., Deng, K., Jocic, R., Lin, Y., Roberts, J., Benites, V. T., Kakumanu, R., Gin, J. W., Chen, Y., Liu, Y., Petzold, C. J., Baidoo, E. E. K., Northen, T. R., Adams, P. D., Katz, L., Yuzawa, S., Keasling, J. D. (2023) Expanding Extender Substrate Selection for Unnatural Polyketide Biosynthesis by Acyltransferase Domain Exchange within a Modular Polyketide Synthase. Journal of the American Chemical Society.

Palmer, M., Covington, J.K., Zhou, EM., Thomas, S.C., Habib, N., Seymour, C.O., Lai, D., Johnston, J., Hashimi, A., Jiao, J.Y., Muok, A.R., Liu, L., Xian, W.D., Zhi, X.Y., Li, M.M., Silva, L.P, Bowen, B.P., Louie, K., Breigel, A., Pett-Ridge, J., Weber, P.K., Tocheva, E. I, Woyke, T., Northen, T. R., Mayali, X., Li, W.J., Hedlund, B.P. (2023) Thermophilic Dehalococcoidia with unusual traits shed light on an unexpected past. ISME J.

McLaughlin, S., Zhalnina, K., Kosina, S., Northen, T. R., Sasse, J. (2023). The core metabolome and root exudation dynamics of three phylogenetically distinct plant species. Nat Commun 14, 1649.

De Raad, M., Koper, K., Deng, K., Bowen, B. P., Maeda, H. A., Northen, T. R. (2023). Mass spectrometry imaging–based assays for aminotransferase activity reveal a broad substrate spectrum for a previously uncharacterized enzyme. Journal of Biological Chemistry.

Chacon, S. S., Karaoz, U., Louie, K, Bowen, B. P, Northen, T. R., Dietterich, L. H., Cusack, D. F., Bouskill, N. (2023) Microbial metabolic response to throughfall exclusion and feedback on soil carbon dynamics along a tropical forest precipitation gradient. EGU23.

Deng, K., Wang, X., Ing, N., Opgenorth, P., de Raad, M., Kim, J., Simmons, B. A., Adams, P. D., Singh, A. K., Lee, T. S., Northen, T. R. (2023). Rapid quantification of alcohol production in microorganisms based on nanostructure-initiator mass spectrometry (NIMS). Analytical Biochemistry.

Ha. N. S., Onely, J. R., Deng, K., Andeer, P., Bowen, B. P., Gupta, K., Kim, P. W., Kuch, N., Kutschke, M., Parker, A., Song, F., Fox, B., Adamn, P. D., de Raad, M., Northen, T. R. (2023). A combinatorial droplet microfluidic device integrated with mass spectrometry for enzyme screening. Royal Society of Chemistry.

Trexler R.V. , Van Goethem M.W. , Goudeau D., Nath N., Malmstrom R. R., Northen T.R., Couradeau E. (2023) BONCAT-FACS-Seq reveals the active fraction of a biocrust community undergoing a wet-up event. Frontiers in Microbiology.

Harwood, T. V., Treen, D., Wang, M., de Jong, W., Northen, T. R., Bowen, B. P. (2023). BLINK: Ultrafast tandem mass spectrometry cosine similarity scoring. bioRxiv.

Vlastimil, N., Andeer, P. F., Bowen, B. P., Ding, Y., Zhalnina, K., Tomaka, C., Golini, A., Kosina, S. M., Northen, T. R. (2023). Reproducible growth of Brachypodium distachyon in fabricated ecosystems (EcoFAB 2.0) reveals that nitrogen form and starvation modulate root exudation. Cold Spring Harbor Laboratory.

Acharya, S. M., Yee, M. O., Diamond, S., Andeer, P. F., Baig, N. F., Aladaesanmi, O. T., Northen, T. R., Banfield, J. F., Chakraborty, R. (2023). Fine scale sampling reveals spatial heterogeneity of rhizosphere microbiome in young Brachypodium plants. bioRxiv.


Coker, J., Zhalnina, K., Marotz, C., Thiruppathy, D., Tjuanta, M., D’Elia, G., Hailu, R., Mahosky, T., Rowan, M., Northen, T. R., Zengler, K. (2022). A reproducible and tunable synthetic soil microbial community provides new insights into microbial ecology. Msystems.

Lin, C., Tian, Y., Nelson-Vasilchick, K., Hague, J., Kakumanu, R., Lee, M. Y., Pidatala, V. R., Trinh, J., De Ben, C. M., Dalton, J., Northen, T. R., Baidoo, E. E., Simmons, B. A., Gladden, J. M., Scown, C. D., Putnam, D. H., Kausch, A. P., Scheller, H. V., Eudes, A. (2022). Engineering sorghum for higher 4-hydroxybenzoic acid content. Metabolic Engineering Communications.

Domeignoz-Horta, L. A., Pold, G., Erb, H. Sebag, D., Verrecchia, E., Northen, T. R., Louie, K., Eloe-Fadrosh, E., Pennacchio, C., Knorr, M. A., Frey, D. F., Melillo, J. M., DeAngelis, K. M. (2022). Substrate availability and not thermal‐acclimation controls microbial temperature sensitivity response to long term warming. Global Change Biology.

Wilhelm, R. C., Barnett, S. E., Swenson, T. L., Youngblut, N. D., Koechli, C. N., Bowen, B. P., Northen, T. R., Buckley, D. H. (2022). Tracing carbon metabolism with stable isotope metabolomics reveals the legacy of diverse carbon sources in soil. Applied and Environmental Microbiology.

Tom, L.M., Aulitto, M., Wu, Y., Deng, K., Gao, Y., Xiao, N., Rodriguez, B. G., Louime, C., Northen, T. R., Eudes, A., Mortimer, J. C., Adams, P. D., Scheller, H. V., Simmons, B. A., Ceja-Navarro, J. A., Singer, S. W. (2022). Low-abundance populations distinguish microbiome performance in plant cell wall deconstruction. Microbiome.

Conway, J. M., Walton, W. G., Salas-González, I., Law, T. F., Lindberg, C. A., Crook, L. E., Kosina, S. M., Fitzparicke, C. R., Lietzan, A. D., Northen, T. R., Jones, C. D., Finkel, O. M., Redinbo, M. R., Dangl, J. L. (2022). Diverse MarR bacterial regulators of auxin catabolism in the plant microbiome. Nature Microbiology.

Palmer, M. Covington, J., Zhou, E., Thomas, S., Habib, N., Seymour, C., Lai, D., Johnston, J., Hashimi, A., Jiao, J., Muok, A., Liu, L., Xian, W., Zhi, X., Li, M., Silva, L., Bowen, B. P., Louie, K., Briegel, A., Pett-Ridge, J., Weber, P., Tocheva, E., Woyke, T., Northen, T. R., Mayali, X., Li, W., Hedlund, B. (2022). Thermophilic Dehalococcoidia with unusual traits shed light on an unexpected past. Research Square.

Howard-Varona, C., Roux, S., Bowen, B.P., Silva, L. P., Lau, R., Schwenck, S. M., Schwartz, S., Woyke, T., Northen, T., Sullivan, M. B., Floge, S. A. (2022) Protist impacts on marine cyanovirocell metabolism. ISME Communications. 2, 94

Kuang, W., Sanow, S., Kelm, J. M., Linpow, M. M., Andeer, P., Kohlheyer, D., Northen, T., Vogel, J. P., Watt, M., Arsova, B. (2022). N-dependent dynamics of root growth and nitrate and ammonium uptake are altered by the bacterium Herbaspirillum seropedicae in the cereal model Brachypodium distachyon. Journal of experimental botany.

Pham, L. T. M., Deng, K., Northen, T., Singer, S., Adams, P., Simmons, B., Sale, K. (2022). Heterologous Expression, Characterization, and Comparison of Laccases from the White Rot Causing Basidiomycete Cerrena Unicolor. Catalysis Research.

de Raad M., Li Y .V., Kuehl J.V., Andeer P.F., Kosina S.M., Hendrickson A., Saichek N. R., Golini A. N., Han L. Z., Wang Y., Bowen B. P., Deutschbauer A. M., Arkin A. P., Chakraborty R., Northen T. R. (2022). A Defined Medium for Cultivation and Exometabolite Profiling of Soil Bacteria. Front. Microbiol. 13:855331. DOI:10.3389/fmicb.2022.855331

Van Goethem, M.W., Couradeau, E., Northen, T.R. (2022). Novel Methods for Studying the Structure and Function of Hot Desert Microorganisms and Their Communities. In: Ramond, JB., Cowan, D.A. (eds) Microbiology of Hot Deserts. Ecological Studies, vol 244. Springer, Cham.

Hu, Y., Andeer, P. F., Zheng, Q., Kosina, S. M., Jardine, K. J., Ding. Y., Han, L. Z., Gao, Y., Zengler, K., Bowen, B. P., Mortimer, J. C., Vogel, J. P., Northen, T. R. (2022). Extensive plant use of exometabolites. bioRxiv.

Van Goethem, M.W., Couradeau, E., Northen, T.R. (2022). Novel Methods for Studying the Structure and Function of Hot Desert Microorganisms and Their Communities. In: Ramond, JB., Cowan, D.A. (eds) Microbiology of Hot Deserts. Ecological Studies, vol 244. Springer, Cham.

Brecht, S., Zhalnina, K., Kosina, S., Northen, T., Sassee, J. (2022). The core metabolome and exudation dynamics of three phylogenetically distinct plant species. Research Square.

Calhoun, S., Kamel, B., Bell, T. A. S, Jrusem C. P. S., Riley, R., Singan, V., Kundee, Y., Cleasner, C. D., Chovatia, M., Sandor, L., Daum, C., Treen, D., Bowen, B. P., Louie, K. B., Northen, T. R., Starkenburg, S. R., Grigoriev, I. V. (2022).  Multi-omics profiling of the cold tolerant Monoraphidium minutum 26B-AM in response to abiotic stress. Algal Research.

Hu, Y., Northen, T.R. (2022) A sweet spot in marine ecosystems. Nat Ecol Evol 6, 847–848.

Howe, A., Bonito, G., Chou, M. Y., Cregger, M. A., Fedders, A., Field, J. L., Martin, H. G., Labbé, J. L., Mechan-Llontop, M. E., Northen, T. R., Shade, A., Tschaplinski, T. J. (2022). Frontiers and Opportunities in Bioenergy Crop Microbiome Research Networks. Phytobiomes Journal.

Treen, D.G.C., Wang, M., Xing, S. et al. SIMILE enables alignment of tandem mass spectra with statistical significance. Nat Commun 13, 2510 (2022).

Ke, J., Robinson, D., Wu, Z., Kuftin, A., Louie, K., Kosina, S., Northen, T., Cheng, J., Yoshikuni, Y. (2022) CRAGE-CRISPR facilitates rapid activation of secondary metabolite biosynthetic gene clusters in bacteria. Cell chemical biology.

Brisson, V. L., Richardy, J., Kosina, S. M., Northen, T. R., Vogel, J. P., Gaudin, A. C. M. (2022). Phosphate Availability Modulates Root Exudate Composition and Rhizosphere Microbial Community in a Teosinte and a Modern Maize Cultivar. Phytobiomes Journal, 6(1), 83–94.

Wang, Y., Northen, T. R. (2022). Small partners, big impacts. Nature Reviews Microbiology20(3), 127.

York, L. M., Cumming, J. R., Trusiak, A., Bonito, G., Haden, A. C., Kalluri, U. C., Tiemann, L. K., Andeer, P. F., Blanc‐Betes, E., Diab, J. H., Favela, A., Germon, A., Gomez‐Casanovas, N., Hyde, C. A., Kent, A. D., Ko, D. K., Lamb, A., Missaoui, A. M., Northen, T. R., . . . Yang, W. H. (2022). Bioenergy Underground: Challenges and opportunities for phenotyping roots and the microbiome for sustainable bioenergy crop production. The Plant Phenome Journal, 5(1).

Young, K. E., Ferrenberg, S., Reibold, R., Reed, S. C., Swenson, T., Northen, T., Darrouzet-Nardi, A. (2022). Vertical movement of soluble carbon and nutrients from biocrusts to subsurface mineral soils. Geoderma, 405, 115495.

Ke, J., Zhao, Z., Coates, C. R., Hadjithomas, M., Kuftin, A., Louie, K., Weller, D., Thomashow, L., Mouncey, N. J., Northen, T. R., Yoshikuni, Y. (2022). Development of platforms for functional characterization and production of phenazines using a multi-chassis approach via CRAGE. Metabolic Engineering69, 188–197.


Kosina, S. M., Rademacher, P., Wetmore, K. M., de Raad, M., Zemla, M., Zane, G. M., Zulovich, J. J., Chakraborty, R., Bowen, B. P., Wall, J. D., Auer, M., Arkin, A. P., Deutschbauer, A. M., & Northen, T. R. (2021). Biofilm Interaction Mapping and Analysis (BIMA) of Interspecific Interactions in Pseudomonas Co-culture Biofilms. Frontiers in Microbiology12.

van Goethem, M. W., Osborn, A. R., Bowen, B. P., Andeer, P. F., Swenson, T. L., Clum, A., Riley, R., He, G., Koriabine, M., Sandor, L., Yan, M., Daum, C. G., Yoshinaga, Y., Makhalanyane, T. P., Garcia-Pichel, F., Visel, A., Pennacchio, L. A., O’Malley, R. C., & Northen, T. R. (2021). Long-read metagenomics of soil communities reveals phylum-specific secondary metabolite dynamics. Communications Biology, 4(1).

Franco, M. E. E., Wisecaver, J. H., Arnold, A. E., Ju, Y., Slot, J. C., Ahrendt, S., Moore, L. P., Eastman, K. E., Scott, K., Konkel, Z., Mondo, S. J., Kuo, A., Hayes, R. D., Haridas, S., Andreopoulos, B., Riley, R., LaButti, K., Pangilinan, J., Lipzen, A., . . . U’Ren, J. M. (2021). Ecological generalism drives hyperdiversity of secondary metabolite gene clusters in xylarialean endophytes. New Phytologist233(3), 1317–1330.

Brisson, V., Mayali, X., Bowen, B., Golini, A., Thelen, M., Stuart, R. K., & Northen, T. R. (2021). Identification of Effector Metabolites Using Exometabolite Profiling of Diverse Microalgae. mSystems, 6(6).

Carrell, A. A., Veličković, D., Lawrence, T. J., Bowen, B. P., Louie, K. B., Carper, D. L., Chu, R. K., Mitchell, H. D., Orr, G., Markillie, L. M., Jawdy, S. S., Grimwood, J., Shaw, A. J., Schmutz, J., Northen, T. R., Anderton, C. R., Pelletier, D. A., & Weston, D. J. (2021). Novel metabolic interactions and environmental conditions mediate the boreal peatmoss-cyanobacteria mutualism. The ISME Journal16(4), 1074–1085.

Petras, D., Phelan, V. V., Acharya, D., Allen, A. E., Aron, A. T., Bandeira, N., Bowen, B. P., Belle-Oudry, D., Boecker, S., Cummings, D. A., Deutsch, J. M., Fahy, E., Garg, N., Gregor, R., Handelsman, J., Navarro-Hoyos, M., Jarmusch, A. K., Jarmusch, S. A., Louie, K., . . . Wang, M. (2021). GNPS Dashboard: collaborative exploration of mass spectrometry data in the web browser. Nature Methods19(2), 134–136.

Pham, L., Deng, K., Northen, T.R. et al. Experimental and theoretical insights into the effects of pH on catalysis of bond-cleavage by the lignin peroxidase isozyme H8 from Phanerochaete chrysosporium. Biotechnol Biofuels 14, 108 (2021).

Ke, J., Robinson, D., Wu, Z. Y., Kuftin, A., Louie, K., Kosina, S., Northen, T., Cheng, J. F., & Yoshikuni, Y. (2021). CRAGE-CRISPR facilitates rapid activation of secondary metabolite biosynthetic gene clusters in bacteria. Cell Chemical Biology.

Jabusch, L. K., Kim, P. W., Chiniquy, D., Zhao, Z., Wang, B., Bowen, B., Kang, A. J., Yoshikuni, Y., Deutschbauer, A. M., Singh, A. K., & Northen, T. R. (2021). Microfabrication of a Chamber for High-Resolution, In Situ Imaging of the Whole Root for Plant–Microbe Interactions. International Journal of Molecular Sciences22(15), 7880.

Ding, Yezhang, Northen, T.R., et al. Getting back to the grass roots: harnessing specialized metabolites for improved crop stress resilience. Current Opinion in Biotechnology, Volume 70 (2021).

Ing, N., Deng, K., Chen, Y. et al. A multiplexed nanostructure-initiator mass spectrometry (NIMS) assay for simultaneously detecting glycosyl hydrolase and lignin modifying enzyme activities. Sci Rep 11, 11803 (2021).

Swift, C. L., Louie, K. B., Bowen, B. P., Olson, H. M., Purvine, S. O., Salamov, A., Mondo, S. J., Solomon, K. V., Wright, A. T., Northen, T. R., Grigoriev, I. V., Keller, N. P., & O’Malley, M. A. (2021). Anaerobic gut fungi are an untapped reservoir of natural products. Proceedings of the National Academy of Sciences118(18), e2019855118.

Swift, C. L., Louie, K. B., Bowen, B. P., Hooker, C. A., Solomon, K. V., Singan, V., Daum, C., Pennacchio, C. P., Barry, K., Shutthanandan, V., Evans, J. E., Grigoriev, I. V., Northen, T. R., & O’Malley, M. A. (2021b). Cocultivation of Anaerobic Fungi with Rumen Bacteria Establishes an Antagonistic Relationship. MBio12(4).

Thomas SC, Payne D, Tamadonfar KO, Seymour CO, Jiao J-Y, Murugapiran SK, Lai D, Lau R, Bowen BP, Silva LP, Louie KB, Huntemann M, Clum A, Spunde A, Pillay M, Palaniappan K, Varghese N, Mikhailova N, Chen I-M, Stamatis D, Reddy TBK, O’Malley R, Daum C, Shapiro N, Ivanova N, Kyrpides NC, Woyke T, Eloe-Fadrosh E, Hamilton TL, Dijkstra P, Dodsworth JA, Northen TR, Li W-J and Hedlund BP (2021) Genomics, Exometabolomics, and Metabolic Probing Reveal Conserved Proteolytic Metabolism of Thermoflexus hugenholtzii and Three Candidate Species From China and Japan. Front. Microbiol. 12:632731.

McGivern, B.B., Tfaily, M.M., Borton, M.A. et al. Decrypting bacterial polyphenol metabolism in an anoxic wetland soil. Nat Commun 12, 2466 (2021).

Lenz, Lenz, R., Louie, K., Sondreli, K., Galanie, S., Chen, J., et al. Metabolic patterns in Septoria canker resistant and susceptible Populus trichocarpa genotypes 24 hours post-inoculation (2021). Phytopathology.

Yee MO, Kim P, Li Y, Singh AK, Northen TR and Chakraborty R (2021) Specialized Plant Growth Chamber Designs to Study Complex Rhizosphere Interactions. Front. Microbiol. 12:625752.

Calhoun, S., Bell, T.A.S., Dahlin, L.R. et al. A multi-omic characterization of temperature stress in a halotolerant Scenedesmus strain for algal biotechnology. Commun Biol 4, 333 (2021).

Singer, E., Vogel, J. P., Northen, T., Mungall, C. J., & Juenger, T. E. (2021). Novel and Emerging Capabilities that Can Provide a Holistic Understanding of the Plant Root Microbiome. Phytobiomes Journal, PBIOMES-05.

Murphy, K.M., Edwards, J., Louie, K.B. et al. Bioactive diterpenoids impact the composition of the root-associated microbiome in maize (Zea mays). Sci Rep 11, 333 (2021).

Morton, J.T., McDonald, D., Aksenov, A.A. et al. Reply to: Examining microbe–metabolite correlations by linear methods. Nat Methods 18, 40–41 (2021).

Pett-Ridge J. et al. (2021) Rhizosphere Carbon Turnover from Cradle to Grave: The Role of Microbe–Plant Interactions. In: Gupta V.V.S.R., Sharma A.K. (eds) Rhizosphere Biology: Interactions Between Microbes and Plants. Rhizosphere Biology. Springer, Singapore.


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Van Goethem, M.W., Swenson, T.L., Trubl, G., Roux, S., Northen, T.R (2019). Characteristics of Wetting-Induced Bacteriophage Blooms in Biological Soil Crust. mBio, 10(6).

Wang, G., Zhao, Z., Ke, J., Engel, Y., Shi, Y., Robinson, D., Bingol, K., Zhang, Z., Bowen, B., Louie, K., Wang, B., Evans, R., Miyamoto, Y., Cheng, K., Kosina, S., de Raad, M., Silva, L., Luhrs, A., Lubbe, A., Hoyt, D.W., Francavilla, C., Otani, H., Deutsch, S., Washton, N.M., Rubin, E.M., Mouncey, N.J., Visel, A., Northen, T., Cheng, J., Bode, H.B., Yoshikuni, Y. (2019). CRAGE enables rapid activation of biosyntehtic gene clusters in undomesticated bacteria. Nature Microbiology, 4, 2498-2510.

Carmody, R.N., Bisanz, J.E., Bowen, B.P., Maurice, C.F., Lyalina, S., Louie, K.B., Treen, D., Chadaideh, K.S., Rekdal, V.M., Bess, E.N., Spanogiannopoulos, P., Ang, Q.Y., Bauer, K.C., Balon, T.W., Pollard, K.S., Northen, T.R., Turnbaugh, P.J. (2019). Cooking shapes the structure and function of the gut microbiome. Nature Microbiology, 4, 2052-2063.

Brisson, V.L., Schmidt, J.E., Northen, T.R., Vogel, J.P., Gaudin, A.C.M. (2019). Impacts of Maize Domestication and Breeing on Rhizosphere Microbial Community Recruitment from a Nutrient Depleted Agricultural Soil. Scientific Reports, 9, 15611.

Couradeau, E., Sasse, J., Goudeau, D., Nath, N., Hazen, T.C., Bowen, B.P., Chakraborty, R., Malmstrom, R.R., Northen, T.R (2019). Probing the active fraction of soil microbiomes using BONCAT-FACS. Nature communications, 10(1), 1-10.

Chevrette, M.G., Carlos-Shanley, C., Louie, K.B., Bowen, B.P., Northen, T.R, Currie, C.R. (2019). Taxonomic and Metabolic Incongruence in the Ancient Genus StreptomycesFrontiers in Microbiology.

Roth, M. S., Gallaher, S. D., Westcott, D. J., Iwai, M., Louie, K. B., Mueller, M., Walter, A., Foflonker, F., Bowen, B., Ataii, N. Song, J., Chen, J., Blaby-Haas, C., Larabell, C., Auer, M., Northen, T. R., Merchant, S. S., Niyogi, K. K. (2019). Regulation of Oxygenic Photosynthesis during Trophic Transitions in the Green Alga Chromochloris zofingiensis. The Plant Cell, 31(3), 579–601.

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Malik, A. A., Swenson, T., Weihe, C., Morrison, E., Martiny, J. B., Brodie, E. L., Northen, T. R., Allison, S. D. (2019). Physiological adaptations of leaf litter microbial communities to long-term drought. BioRxiv, 631077.

Opgenorth, P., Costello, Z., Okada, T.,  Goyal, G., Chen, Y., Gin, J., Benites, V., de Raad, M., Northen, T. R., Deng, K., Deutsch, S., Baidoo, E. E. K., Petzold, C. J., Hillson, N. J., Martin, H. G., Beller, H. R. (2019). Lessons from two Design-Build-Test-Learn cycles of dodecanol production in Escherichia coli aided by machine learning. ACS Synthetic Biology, acssynbio.9b00020.

Erbilgin, O., Rübel, O., Louie, K. B., Trinh, M., Raad, M. De, Wildish, T., Udwary, D., Hoover, C., Deutsch, S., Northen, T. R., Bowen, B. P. (2019). MAGI: A Method for Metabolite Annotation and Gene Integration. ACS Chemical Biology, 14(4), 704–714.

Sasse, J., Kant, J., Cole, B. J., Klein, A. P., Arsova, B., Schlaepfer, P., Gao, J., Lewald, K., Zhalnina, K., Kosina, S., Bowen, B. P., Treen, D., Vogel, J., Visel, A., Watt, M., Dangl, J. L., Northen, T. R. (2019). Multilab EcoFAB study shows highly reproducible physiology and depletion of soil metabolites by a model grass. New Phytologist, 222(2), 1149–1160.

Diamond, S., Andeer, P. F., Li, Z., Crits-Christoph, A., Burstein, D., Anantharaman, K., Lane, K. R., Thomas, B. C., Pan, C., Northen, T. R., Banfield, J. F. (2019). Mediterranean grassland soil C–N compound turnover is dependent on rainfall and depth, and is mediated by genomically divergent microorganisms. Nature Microbiology.

de Rond, T., Gao, J., Zargar, A., de Raad, M., Cunha, J., Northen, T. R., & Keasling, J. D. (2019). A high‐throughput mass spectrometric enzyme activity assay enabling the discovery of cytochrome P450 biocatalysts. Angewandte Chemie, ange.201901782.

Roux, S., Trubl, G., Goudeau, D., Nath, N., Couradeau, E., Ahlgren, N. A., Zhan, Y., Marsan, D., Chen, F., Fuhrman, J. A., Northen, T. R., Sullivan, M. B., Rich, V. I., Malmstrom, R. R., Eloe-Fadrosh, E. A. (2019). Optimizing de novo genome assembly from PCR-amplified metagenomes. PeerJ, 7, e6902.

Guzmán, G. I., Sandberg, T. E., LaCroix, R. A., Nyerges, Á., Papp, H., de Raad, M., King, Z. A., Hefner, Y., Northen, T. R., Notebaart, R. A., Pal, C., Palsson, B. O., Papp, B., Feist, A. M. (2019). Enzyme promiscuity shapes adaptation to novel growth substrates. Molecular Systems Biology, 15(4), e8462.

Brisson, V., Schmidt, J., Northen, T. R., Vogel, J. P., & Gaudin, A. (2019). A New Method to Correct for Habitat Filtering in Microbial Correlation Networks. Frontiers in Microbiology, 10(March), 1–10.


Kosina, S. M., Greiner, A. M., Lau, R. K., Jenkins, S., Baran, R., Bowen, B. P., & Northen, T. R. (2018). Web of microbes (WoM): a curated microbial exometabolomics database for linking chemistry and microbes. BMC Microbiology, 18(1).

de Raad, M., Northen, T. R., & Bowen, B. P. (2018). Analysis and Interpretation of Mass Spectrometry Imaging Datasets. Comprehensive Analytical Chemistry, 369–386.

Porcar, M., Louie, K. B., Kosina, S. M., Van Goethem, M. W., Bowen, B. P., Tanner, K., & Northen, T. R. (2018). Microbial ecology on solar panels in Berkeley, CA, United States. Frontiers in Microbiology, 9(DEC), 1–14.

Gao, J., Sasse, J., Lewald, K. M., Zhalnina, K., Cornmesser, L. T., Duncombe, T. A., Yoshikuni, Yi., Vogel, J. P., Firestone, M. K., Northen, T. R. (2018). Ecosystem Fabrication (EcoFAB) Protocols for The Construction of Laboratory Ecosystems Designed to Study Plant-microbe Interactions. Journal of Visualized Experiments, (134), 1–16.

Karaoz, U., Couradeau, E., da Rocha, U. N., Lim, H.-C., Northen, T., Garcia-Pichel, F., & Brodie, E. L. (2018). Large Blooms of Bacillales (Firmicutes) Underlie the Response to Wetting of Cyanobacterial Biocrusts at Various Stages of Maturity . MBio, 9(2), e01366-16.

Zhalnina, K., Zengler, K., Newman, D., & Northen, T. R. (2018). Need for Laboratory Ecosystems To Unravel the Structures. MBio, 9(4), 1–8.

Venturelli, O. S., Carr, A. C., Fisher, G., Hsu, R. H., Lau, R., Bowen, B. P., Hromada, S., Northen, T., Arkin, A. P. (2018). Deciphering microbial interactions in synthetic human gut microbiome communities. Molecular Systems Biology, 14(6), e8157.

Sasse, J., Martinoia, E., & Northen, T. (2018). Feed Your Friends: Do Plant Exudates Shape the Root Microbiome? Trends in Plant Science, 23(1), 25–41.

Deng, K., Zeng, J., Cheng, G., Gao, J., Sale, K. L., Simmons, B. A., Singh, A. K., Adams, P. D., Northen, T. R. (2018). Rapid characterization of the activities of lignin-modifying enzymes based on nanostructure-initiator mass spectrometry (NIMS). Biotechnology for Biofuels, 11(1).

Couradeau, E., Sasse, J., Goudeau, D., Nath, N., Hazen, T. C., Bowen, B. P., Malmstrom, R. R., Northen, T. R. (2018). Study of Oak Ridge soils using BONCAT-FACS-Seq reveals that a large fraction of the soil microbiome is active. BioRxiv, 404087.

Swenson, T. L., Karaoz, U., Swenson, J. M., Bowen, B. P., & Northen, T. R. (2018). Linking soil biology and chemistry in biological soil crust using isolate exometabolomics. Nature Communications, 9(1).

Zhalnina, K., Louie, K. B., Hao, Z., Mansoori, N., Da Rocha, U. N., Shi, S., Cho, H., Karaoz, U., Loque, D., Bowen, B. P., Firestone, M. K., Northen, T. R., Brodie, E. L. (2018). Dynamic root exudate chemistry and microbial substrate preferences drive patterns in rhizosphere microbial community assembly. Nature Microbiology, 3(4), 470–480.

Swenson, T. L., Couradeau, E., Bowen, B. P., De Philippis, R., Rossi, F., Mugnai, G., & Northen, T. R. (2018). A novel method to evaluate nutrient retention by biological soil crust exopolymeric matrix. Plant and Soil, 429(1–2), 53–64.

Iwai, K., Ando, D., Kim, P. W., Gach, P. C., Raje, M., Duncomb, T. A., Heinemann, J. V., Northen, T. R., Martin, H. G., Hillson, N. J., Adamsn, P. D., Singh, A. K. (2018). Automated flow-based/digital microfluidic platform integrated with onsite electroporation process for multiplex genetic engineering applications. Proceedings of the IEEE International Conference on Micro Electro Mechanical Systems (MEMS), 2018January(January), 1229–1232.

Duncombe, T. A., Raad, M. De, Bowen, B. P., Singh, A. K., & Northen, T. R. (2018). Insulator Nanostructure Desorption Ionization Mass Spectrometry [Article-commentary]. Analytical Chemistry, 90(16), 9657–9661.

Jose, N. A., Lau, R., Swenson, T. L., Klitgord, N., Garcia-Pichel, F., Bowen, B. P., Baran, R., Northen, T. R. (2018). Flux balance modeling to predict bacterial survival during pulsed-activity events. Biogeosciences, 15(7), 2219–2229.

Coates, R. C., Bowen, B. P., Oberortner, E., Thomashow, L., Hadjithomas, M., Zhao, Z., Ke., J., Silva, L., Louie, K., Wang, G., Robinson, D., Tarver, A., Hamilton, M., Lubbe, A., Feltcher, M., Dangl, J., Pati, A., Weller, D., Northen, T. R., Cheng, J., Mouncey, N., Deutsch, S., Yoshikuni, Y. (2018). An integrated workflow for phenazine-modifying enzyme characterization. Journal of Industrial Microbiology and Biotechnology, 45(7), 567–577.

Couradeau, E., Felde, V. J. M. N. L., Parkinson, D., Uteau, D., Rochet, A., Cuellar, C., Winegar, G., Peth, S., Northen, T. R., Garcia-Pichel, F. (2018). In Situ X-Ray Tomography Imaging of Soil Water and Cyanobacteria From Biological Soil Crusts Undergoing Desiccation. Frontiers in Environmental Science, 6(June).


Zhou, A., Lau, R., Baran, R., Ma, J., von Netzer, F., Shi, W., Gorman-Lewis, D., Kempher, M. L., He, Z., Qin, Y., Shi, Z., Zane, G. M., Wu, L., Bowen, B. P., Northen, T. R., Hillesland, K. L., Stahl, D. A., Wall, J. D., Arkin, A. P., Zhou, J. (2017). Key Metabolites and Mechanistic Changes for Salt Tolerance in an Experimentally Evolved Sulfate-Reducing Bacterium, Desulfovibrio vulgaris. mBio, 8(6).

Erbilgin, O., Bowen, B. P., Kosina, S. M., Jenkins, S., Lau, R. K., & Northen, T. R. (2017). Dynamic substrate preferences predict metabolic properties of a simple microbial consortium. BMC Bioinformatics, 18(1), 57.

Lubbe, A., Bowen, B. P., & Northen, T. (2017). Exometabolomic Analysis of Cross-Feeding Metabolites. Metabolites, 7(4).

Eudes, A., Dutta, T., Deng, K., Jacquet, N., Sinha, A., Benites, V T., Baidoo E E K., Richel A, Sattler S E, Northen T R, Singh S, Simmons B A, Loqué D. (2017). SbCOMT (Bmr12) is involved in the biosynthesis of tricin-lignin in sorghum. PloS One, 12(6), e0178160.

Mondo, S. J., Dannebaum, R. O., Kuo, R. C., Louie, K. B., Bewick, A. J., LaButti, K., Haridas S, Kuo A, Salamov A, Ahrendt S R, Lau R, Bowen B P, Lipzen A, Sullivan W, Andreopoulos B, Clum A, Lindquist E, Daum C, Northen T R, Kunde Ramamoorthy G, Schmitz R J, Gryganskyi A, Culley D, Magnuson J, James T Y, O’Malley M. A., Starich J. E., Spatafora J. W., Visel A., Grigoriev I. V. (2017). Widespread adenine N6-methylation of active genes in fungi. Nature Genetics, 49(6), 964–968.

Gao, J., Louie, K. B., Steinke, P., Bowen, B. P., Raad, M. de, Zuckermann, R. N., Siuzdak, G., Northen, T. R. (2017). Morphology-Driven Control of Metabolite Selectivity Using Nanostructure-Initiator Mass Spectrometry. Analytical Chemistry, 89(12), 6521–6526.

de Raad, M., de Rond, T., Rübel, O., Keasling, J. D., Northen, T. R., & Bowen, B. P. (2017). OpenMSI Arrayed Analysis Toolkit: Analyzing Spatially Defined Samples Using Mass Spectrometry Imaging. Analytical Chemistry, 89(11), 5818–5823.

Xiong, Y., Wu, V. W., Lubbe, A., Qin, L., Deng, S., Kennedy, M., Bauer, D., Singan, V. R., Barry, K., Northen, T. R., Grigoriev, I. V., Glass, N. L. (2017). A fungal transcription factor essential for starch degradation affects integration of carbon and nitrogen metabolism. PLoS Genetics, 13(5), e1006737.

Baran, R., Lau, R., Bowen, B. P., Diamond, S., Jose, N., Garcia-Pichel, F., & Northen, T. R. (2017). Extensive Turnover of Compatible Solutes in Cyanobacteria Revealed by Deuterium Oxide (D2O) Stable Isotope Probing. ACS Chemical Biology, 12(3), 674–681.

Swenson, T. L., Couradeau, E., Bowen, B. P., De Philippis, R., Rossi, F., Mugnai, G., & Northen, T. R. (2017). A novel method to evaluate nutrient retention by biological soil crust exopolymeric matrix. Plant and Soil.

Jenkins, S., Swenson, T. L., Lau, R., Rocha, A. M., Aaring, A., Hazen, T. C., Chakraborty, R., Northen, T. R. (2017). Construction of Viable Soil Defined Media Using Quantitative Metabolomics Analysis of Soil Metabolites. Frontiers in Microbiology, 8, 2618.

Venturelli, O. S., Carr, A. C., Fisher, G., Hsu, R. H., Lau, R., Bowen, B. P., Northen, T. R., Arkin, A. P. (2017). Deciphering microbial interactions in synthetic human gut microbiome communities. bioRxiv.

Erbilgin, O., Ruebel, O., Louie, K. B., Trinh, M., de Raad, M., Wildish, T., Udwary, D. W., Hoover, C. A., Deutsch, S., Northen, T. R., Bowen, B. P. (2017). MAGI: A Bayesian-like method for metabolite, annotation, and gene integration. bioRxiv.

Heinemann, J., Deng, K., Shih, S. C. C., Gao, J., Adams, P. D., Singh, A. K., and Northen, T. R. (2017) On-chip integration of droplet microfluidics and nanostructure-initiator mass spectrometry for enzyme screening. Lab Chip 17, 323–331.

Yuzawa, S., Deng, K., Wang, G., Baidoo, E. E. K., Northen, T. R., Adams, P. D., Katz, L., and Keasling, J. D. (2017) Comprehensive in Vitro Analysis of Acyltransferase Domain Exchanges in Modular Polyketide Synthases and Its Application for Short-Chain Ketone Production. ACS Synth. Biol. 6, 139–147.

Walker, J. A., Pattathil, S., Bergeman, L. F., Beebe, E. T., Deng, K., Mirzai, M., Northen, T. R., Hahn, M. G., and Fox, B. G. (2017) Determination of glycoside hydrolase specificities during hydrolysis of plant cell walls using glycome profiling. Biotechnol. Biofuels 10.

Duncombe, T. A., Adams, P., Singh, A., & Northen, T. (2017). Parallel microarraying of microfluidic droplets for high-throughput integration with matrix-assisted laser desorption ionization mass spectrometry. 2017 IEEE 30th International Conference on Micro Electro Mechanical Systems (MEMS). Published.

Duncombe, T. A., Adams, P., Singh, A., & Northen, T. (2017). Self-assembled gold nanoparticle film for nanostructure-initiator mass spectrometry with passive on-line salt fractionation. 2017 IEEE 30th International Conference on Micro Electro Mechanical Systems (MEMS). Published.


Montenegro-Burke, J. R., Phommavongsay, T., Aisporna, A. E., Huan, T., Rinehart, D., Forsberg, E., Poole, F. L., Thorgersen, M. P., Adams, M. W. W., Krantz, G., Fields, M. W., Northen, T. R., Robbins, P. D., Niedernhofer, L. J., Lairson, L., Benton, H. P., & Siuzdak, G. (2016). Smartphone Analytics: Mobilizing the Lab into the Cloud for Omic-Scale Analyses. Analytical Chemistry, 88(19), 9753–9758.

Hiras, J., Wu, Y. W., Deng, K., Nicora, C. D., Aldrich, J. T., Frey, D., Kolinko, S., Robinson, E. W., Jacobs, J. M., Adams, P. D., Northen, T. R., Simmons, B. A., and Singer, S. W. (2016) Comparative community proteomics demonstrates the unexpected importance of actinobacterial glycoside hydrolase family 12 protein for crystalline cellulose hydrolysis. MBio 7, 1–9.

Wang, M., Carver, J. J., Phelan, V. V., Sanchez, L. M., Garg, N., Peng, Y., Nguyen, D. D., Watrous, J., Kapono, C. A., Luzzatto-Knaan, T., Porto, C., Bouslimani, A., Melnik, A. V., Meehan, M. J., Liu, W. T., Crüsemann, M., Boudreau, P. D., Esquenazi, E., Sandoval-Calderón, M., . . . Bandeira, N. (2016). Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking. Nature Biotechnology, 34(8), 828–837.

Bouskill, N. J., Wood, T. E., Baran, R., Ye, Z., Bowen, B. P., Lim, H., Zhou, J., Nostrand, J. D. V., Nico, P., Northen, T. R., Silver, W. L., & Brodie, E. L. (2016). Belowground Response to Drought in a Tropical Forest Soil. I. Changes in Microbial Functional Potential and Metabolism. Frontiers in Microbiology7.

Bouskill, N. J., Wood, T. E., Baran, R., Hao, Z., Ye, Z., Bowen, B. P., Lim, H. C., Nico, P. S., Holman, H. Y., Gilbert, B., Silver, W. L., Northen, T. R., & Brodie, E. L. (2016). Belowground Response to Drought in a Tropical Forest Soil. II. Change in Microbial Function Impacts Carbon Composition. Frontiers in Microbiology7.

Shih, P. M., Vuu, K., Mansoori, N., Ayad, L., Louie, K. B., Bowen, B. P., Northen, T. R., & Loqué, D. (2016). A robust gene-stacking method utilizing yeast assembly for plant synthetic biology. Nature Communications, 7(1).

Kosina, S. M., Danielewicz, M. A., Mohammed, M., Ray, J., Suh, Y., Yilmaz, S., Singh, A. K., Arkin, A. P., Deutschbauer, A. M., and Northen, T. R. (2016) Exometabolomics Assisted Design and Validation of Synthetic Obligate Mutualism. ACS Synth. Biol. 5, 569–576.

Lubbe, A., and Northen, T. (2016) Exometabolomics for Linking Soil Carbon to Microbial Communities, in Microbial Metabolomics (Al., D. J. B. et, Ed.), pp 119–145. Springer International Publishing.

Gao J, de Raad M, Bowen BP, Zuckermann RN, Northen TR. Application of black silicon for nanostructure-initiator mass spectrometry. Analytical Chemistry, 2016 88(3) 1625-1630

Walker JA, Takasuka TE, Deng K, Bianchetti CM, Udell HS, Prom BM, Kim H, Adams PD, Northen TR, Fox BG. Multifunctional cellulase catalysis targeted by fusion to different carbohydrate-binding modules. Biotechnol Biofuels. 2015 Dec 21;8:220.

Deng K, Takasuka TE, Bianchetti CM, Bergeman LF, Adams PD, Northen TR, Fox BG. Use of Nanostructure-Initiator Mass Spectrometry to Deduce Selectivity of Reaction in Glycoside Hydrolases. Front Bioeng Biotechnol. 2015 Oct 27;3:165.

de Raad M, Fischer CR, Northen TR. High-throughput platforms for metabolomics. Curr Opin Chem Biol. 2016 Feb;30:7-13.

Deng K, Guenther JM, Gao J, Bowen BP, Tran H, Reyes-Ortiz V, Cheng X, Sathitsuksanoh N, Heins R, Takasuka TE, Bergeman LF, Geertz-Hansen H, Deutsch S, Loqué D, Sale KL, Simmons BA, Adams PD, Singh AK, Fox BG, Northen TR. Development of a High Throughput Platform for Screening Glycoside Hydrolases Based on Oxime-NIMS. Front Bioeng Biotechnol. 2015 Oct 13;3:153.

Couradeau, E., Karaoz, U., Lim, H. C., Nunes Da Rocha, U., Northen, T., Brodie, E., & Garcia-Pichel, F. (2016). Bacteria increase arid-land soil surface temperature through the production of sunscreens. Nature Communications7(1).

Butterfield, C. N., Li, Z., Andeer, P. F., Spaulding, S., Thomas, B. C., Singh, A., Hettich, R. L., Suttle, K. B., Probst, A. J., Tringe, S. G., Northen, T., Pan, C., & Banfield, J. F. (2016). Proteogenomic analyses indicate bacterial methylotrophy and archaeal heterotrophy are prevalent below the grass root zone. PeerJ4, e2687.

Mori, H., Bhat, R., Bruni-Cardoso, A., Chen, E. I., Jorgens, D. M., Coutinho, K., Louie, K., Bowen, B. B., Inman, J. L., Tecca, V., Lee, S. J., Becker-Weimann, S., Northen, T., Seiki, M., Borowsky, A. D., Auer, M., & Bissell, M. J. (2016). New insight into the role of MMP14 in metabolic balance. PeerJ4, e2142.

Blaser, M. J., Cardon, Z. G., Cho, M. K., Dangl, J. L., Donohue, T. J., Green, J. L., Knight, R., Maxon, M. E., Northen, T. R., Pollard, K. S., & Brodie, E. L. (2016). Toward a Predictive Understanding of Earth’s Microbiomes to Address 21st Century Challenges. MBio7(3).

Silva, L. P., & Northen, T. R. (2015). Exometabolomics and MSI: deconstructing how cells interact to transform their small molecule environment. Current Opinion in Biotechnology, 34, 209–216.


Baran R, Brodie EL, Mayberry-Lewis J, Hummel E, Nunes Da Rocha U, Chakraborty R, Bowen BP, Karaoz U, Cadillo-Quiroz H, Garcia-Pichel F, Northen TR. Exometabolite niche partitioning among sympatric soil bacteria. Nature Communications, 2015 6(6):8289.

Ceja-Navarro, J. A., F. E. Vega, U. Karaoz, Z. Hao, S. Jenkins, H. C. Lim, P. Kosina, F. Infante, T. R. Northen, and E. L. Brodie. Gut microbiota mediate caffeine detoxification in the primary insect pest of coffee. Nature Communications, 2015, 6:7618.

Yee Ngan CY, Wong CH, Choi C, Yoshinaga Y, Louie K, Jia J, Chen C, Bowen B, Cheng H, Leonelli L, Kuo R, Baran R, JGarcía-Cerdán J,Pratap A, Mei Wang1, Joanne Lim1, Hope Tice1, Daum C, Xu J, Northen TR, Visel A, Bristow J, Niyogi K, Wei CL. Lineage-Specific Chromatin Signatures Reveal a Regulator of Lipid Metabolism in Microalgae. Nature Plants 2015, 1:15107,

Ulisses Nunes da Rocha, Hinsby Cadillo-Quiroz, Ulas Karaoz, Lara Rajeev, Niels Klitgord, Sean Dunn, Viet Truong, Mayra Buenrostro, Benjamin Paul Bowen, Ferran Garcia-Pichel, Aindrila Mukhopadhyay, Trent Russell Northen*, Eoin L Brodie*. Isolation of a significant fraction of non-phototroph diversity from a desert Biological Soil Crust. Frontiers in Microbiology. 2015

Silva L, Northen TR. Exometabolomics and MSI: deconstructing how cells interact to transform their small molecule environment. Current Opinion in Biotechnology. 2015 34, 209-216

Bowen B*, Yao Y, Sun T, Wang T, Ruebel O, Northen T. Analysis of metabolomics datasets with high-performance computing and Metabolite Atlases. Metabolites, 2015, Metabolites 5 (3) 431-442.

Swenson, T. L., Jenkins, S., Bowen, B. P., and Northen, T. R. (2015) Untargeted soil metabolomics methods for analysis of extractable organic matter. Soil Biol. Biochem. 80, 189–198.

Swenson, T. L., Bowen, B. P., Nico, P. S., and Northen, T. R. (2015) Competitive sorption of microbial metabolites on an iron oxide mineral. Soil Biol. Biochem. 90, 34–41.

Kurczy M., Northen T., Trauger, S.A., Siuzdak, G. Nanostructure Imaging Mass Spectrometry: The Role of Fluorocarbons in Metabolite Analysis and the Road to Yoctomole Level Sensitivity. Methods in Mol. Bio. , 2015 1203, 141-149.

Castellanos-Martín, Castillo-Lluva, del Mar Sáez-Freire, Blanco-Gómez, Hontecillas-Prieto, Patino-Alonso, Galindo-Villardon, Pérez del Villar, Carmen Martín-Seisdedos2,6, María Isidoro-Garcia, del Mar Abad-Hernández, Cruz-Hernández, Rodríguez-Sánchez, González-Sarmiento, Alonso-López, De Las Rivas, García-Cenador, Lee, Bowen, Reindl, Northen*, Mao*, Pérez-Losada* Unraveling heterogeneous susceptibility and the evolution of breast cancer by a systems biology approach. Genome Biology 2015 16, 40 2-23.

Sylvie Miquel, Marion Leclerc, rebeca Martin, Florian Chain, Marion Lenoir, Sébastien Raguideau, Sylvie Hudault, Chantal Bridonneau, Trent Northen, Benjamin Bowen, Luis G. Bermúdez-Humarán, Harry Sokol, Muriel Thomas, and Philippe Langella. Identification of metabolic signatures linked to anti-inflammatory effects of Faecalibacterium prausnitzii mBio 2015, 6 (2)

De Rond T, Danielwicz M, Northen T. High throughput screening of enzyme activity with mass spectrometry imaging. Current Opinion in Biotechnology. Current opinion in biotechnology 2015 31, 1-9.


Deng K, Takasuka TE, Heins R, Cheng X, Bergeman LF, Shi J, Aschenbrener R, Deutsch S, Singh S, Sale KL, Simmons BA, Adams PD, Singh AK, Fox BG, Northen TR. Rapid Kinetic Characterization of Glycosyl hydrolases (GHs) based on Oxime Derivatization and Nanostructure-Initiator Mass Spectrometry (NIMS). ACS Chemical Biology 2014, 9(7), 1470-1479. (Cover)

Heins R, Cheng X, Nath S, Deng K, Bowen B; Chivian D, Datta S, Friedland G, D’Haeseleer P, Wu D, Tran-Gyamfi M, Scullin C, Singh S, Shi W, Hamilton M, Bendall M, Sczyrba A, Thompson J, Feldman T, Guenther J, Gladden J, Cheng JF, Adams P, Rubin E, Simmons BA, Sale K, Northen, T, Deutsch S. Phylogenomic Guided Identification of Industrially Relevant GH1 β-Glucosidases Through Coupled DNA Synthesis and Nanostructure-Initiator Mass Spectrometry. ACS Chemical Biology 2014, 19(9), 2082-91.

Vandehey, Nicholas; Brodie, Eoin; Northen, Trent; O’Neil, James. Non-invasive Mapping of Photosynthetic Heterogeneity in Biological Soil Crusts by Positron Emission Tomography: Carbon Fixation. Environmental Science & Technology Letters, 2014, 1(10) 393-398.

Berleman J, Allen S, Danielewicz M, Remis J, Gorur A, Cunha J, Hadi M, Zusman D, Northen T, Witkowska H. Ewa, Manfred Auer, The Lethal Cargo of Myxococcus xanthus Outer Membrane Vesicles, Frontiers in Microbiology 2014, 5, 274, 1-11.

Heins, R. A., Cheng, X., Nath, S., Deng, K., Bowen, B. P., Chivian, D. C., Datta, S., Friedland, G. D., D’Haeseleer, P., Wu, D., Tran-Gyamfi, M., Scullin, C. S., Singh, S., Shi, W., Hamilton, M. G., Bendall, M. L., Sczyrba, A., Thompson, J., Feldman, T., . . . Deutsch, S. (2014). Phylogenomically Guided Identification of Industrially Relevant GH1 β-Glucosidases through DNA Synthesis and Nanostructure-Initiator Mass Spectrometry. ACS Chemical Biology9(9), 2082–2091.

Vandehey, N. T., Northen, T. R., Brodie, E. L., & O’Neil, J. P. (2014). Noninvasive Mapping of Photosynthetic Heterogeneity in Biological Soil Crusts by Positron Emission Tomography: Carbon Fixation. Environmental Science & Technology Letters1(10), 393–398.

Deng, K., Takasuka, T. E., Heins, R., Cheng, X., Bergeman, L. F., Shi, J., Aschenbrener, R., Deutsch, S., Singh, S., Sale, K. L., Simmons, B. A., Adams, P. D., Singh, A. K., Fox, B. G., & Northen, T. R. (2014). Rapid Kinetic Characterization of Glycosyl Hydrolases Based on Oxime Derivatization and Nanostructure-Initiator Mass Spectrometry (NIMS). ACS Chemical Biology9(7), 1470–1479.

Louie, K. B., & Northen, T. R. (2014). Metabolic Imaging Using Nanostructure-Initiator Mass Spectrometry (NIMS). Methods in Molecular Biology, 313–329.


Oliver Rübel, Annette Greiner, Shreyas Cholia, Katherine Louie, E. Wes Bethel, Trent R. Northen, and Benjamin P. Bowen, OpenMSI: High-performance web-based visualization, analysis and management of mass spectrometry imaging data, Analytical Chemistry, 2013 85(21):10354-61.

Baran R, Bowen BP, Price MN, Arkin AP, Deutschbauer AM, Northen TR. Metabolic Footprinting of Mutant Libraries To Map Metabolite Utilization to Genotype. ACS Chemical Biology. 2013, 8 (1), 189-199.

Mosier AC*, Justice NB*, Bowen BP, Baran R, Thomas BC, Northen TR, Banfield JF. Metabolites associated with adaptation of microorganisms to an acidophilic, metal-rich environment identified by stable isotope enabled metabolomics. 2013 Mar 12;4(2):e00484-12 PMCID: PMC3604775.

De Rond T, Peralta-Yahya P, Cheng X, Northen TR, Keasling JD. Versatile synthesis of probes for high-throughput enzyme activity screening. Anal Bioanl Chemistry, 2013 May;405(14):4969-73.

Ryan P. McAndrew, Joshua Park, Wolfgang Reindl, Gregory D. Friedland, Patrik D’haeseleer, Trent Northen, Kenneth L. Sale, Blake A. Simmons, and Paul D. Adams. From soil to structure: a novel dimeric family 3 β-glucosidase isolated from compost using metagenomics. Journal of Biochemistry, 2013,288(21):14985-92.

Louie KB, Bowen BP, McAlhany S, Huang Y, Mao JH, Hellerstein M and Northen TR Kinetic mass spectrometry imaging for in situ kinetic histochemistry, Nature Scientific Reports, 2013 Apr 15;3:1656 PMCID: PMC3625901.

Ho JC, Storm P, Rydström A, Bowen B, Alsin F, Sullivan L, Ambite I, Mok KH, Northen T, Svanborg C. Lipids as tumoricidal components of human alpha-lactalbumin made leathal to tumor cells (HAMLET): unique and shared effects on signaling and death. J Biol Chem. 2013 Jun 14;288(24):17460-71. Epub 2013 Apr 29.

Rajeev L, Nunes da Rocha U, Klitgord N, Luning EG, Fortney J, Axen SP, Shih PM, Bouskill NJ, Bowen BP, Kerfield C, Ferran Garcia-Pichel F, Brodie EL, Northen TR*, Mukhopadhyay, A* Dynamic cyanobacterial response to hydration and dehydration in a desert biological soil crust, ISME Journal, 2013 7, 2178–2191;

Fischer CR, Bowen BP, Pan C, Northen TR, Banfield JF Stable-isotope probing reveals hydrogen isotope fractionation in proteins and lipids in a microbial community are different and species-specific, ACS Chemical Biology 2013, 8 (8), 1755–1763.

Baran, R, Northen, T. Robust Automated Mass Spectra Interpretation and Chemical Formula Calculation Using Mixed Integer Linear Programming. Analytical Chemistry Anal. Chem., 2013, 85 (20), pp 9777–9784.

Baran R, Ivanova N, Jose N, Garcia-Pichel F, Kyrpides N, Gugger M, Northen T. Functional genomics of novel secondary metabolites from diverse cyanobacteria using untargeted metabolomics. Marine Drugs 2013, 11(10), 3617-3631;

Katherine B. Louie, Benjamin P. Bowen, Xiaoliang Cheng, James Berleman, Romy Chakraborty, Adam Deutschbauer, Adam Arkin and Trent R. Northen. “Replica-extraction-transfer” for nanostructure-initiator mass spectrometry imaging of acoustically printed bacteria and microbial communities, Analytical Chemistry 2013, 85(22) 10856-62.

Cheng, X., Hiras, J., Deng, K., Bowen, B., Simmons, B. A., Adams, P. D., Singer, S. W., & Northen, T. R. (2013). High throughput nanostructure-initiator mass spectrometry screening of microbial growth conditions for maximal β-glucosidase production. Frontiers in Microbiology4.


Storm, P; Aits, S; Puthia, MK; Urbano, A; Northen, T; Powers, S; Bowen, B; Chao, Y; Reindl, W; Lee, DY; Sullivan, NL; Zhang, L; Trulsson, M; Yang, H; Watson, JD; and Svanborg; C. Conserved features of cancer cells define their sensitivity to HAMLET-induced death; c-Myc and glycolysis. Oncogene 30, 4765-4779.

Deng K,George KW, Reindl W, Keasling JD, Adams PA, Lee TS, Singh AK, Northen TR, Encoding substrates with mass tags to resolve stereospecific reactions using Nimzyme, Rapid Comm. Mass Spectrometry2012 Mar 30;26(6):611-5.

Fischer CR, Wilmes P, Bowen BP, Northen TR, Banfield JF. Deuterium Exchange Metabolomics Identifies N-Methyl lyso Phosphatidylethanolamines As Abundant Lipids in Acidophilic Mixed Microbial Communities. 2012 8 (4) 566-578.

Patti G.J, Tautenhahn R., Fonslow B.R., Cho Y., Deutschbauer A., Arkin A., Northen T., Siuzdak G. Meta-Analysis of Global Metabolomics and Proteomics Data to Link Alterations with Phenotype Spectroscopy (cover article), 2011, 26(3), 151-154

Greving M, Cheng K, Reindl W, Bowen B, Deng D, Louie K, Nyman M, Cohen J, Singh A, Simmons B, Adams P, Siuzdak G, and Northen T Acoustic deposition with NIMS as a high throughput enzyme activity assay, Anal Bioanl Chemistry 2012 May;403(3):707-11. Epub 2012 Mar 10.

Reindl W, Deng K, Cheng X, Singh AK, Simmons B, Adams P, Northen T Nanostructure-Initiator Mass Spectrometry (NIMS) for the Analysis of Enzyme Activities, Curr. Protocols in Chem. Biology, 2012, 4:123‐142.

Lee DY, Platt V, Bowen B, Louie K, Canaria C, McMurray C, Northen T. Resolving brain regions using nanostructure initiator mass spectrometry imaging of phospholipids. Integrative Biology 2012, 4 (6), 693 – 699.

Lee DY, Bowen B, Louie K, Nguyen, D, Parsa S, Huang Y, Mao JH, Northen T. Low-dose ionizing radiation-induced blood plasma metabolic response in a diverse genetic mouse population. Radiation Research, 2012 Dec;178(6):551-5.

Kamennaya, N., Ajo-Franklin, C., Northen, T., & Jansson, C. (2012). Cyanobacteria as Biocatalysts for Carbonate Mineralization. Minerals2(4), 338–364.


Baran, R., Bowen, B. P., & Northen, T. R. (2011). Untargeted metabolic footprinting reveals a surprising breadth of metabolite uptake and release by Synechococcus sp. PCC 7002. Molecular BioSystems, 7(12), 3200.

Reindl, W., Deng, K., Gladden, J. M., Cheng, G., Wong, A., Singer, S. W., Singh, S., Lee, J. C., Yao, C. H., Hazen, T. C., Singh, A. K., Simmons, B. A., Adams, P. D., & Northen, T. R. (2011). Colloid-based multiplexed screening for plant biomass-degrading glycoside hydrolase activities in microbial communities. Energy & Environmental Science4(8), 2884.

Bowen, B. P., Fischer, C. R., Baran, R., Banfield, J. F., & Northen, T. (2011). Improved genome annotation through untargeted detection of pathway-specific metabolites. BMC Genomics12(Suppl 1), S6.

Northen, T. R. (2011). The Small-Molecule Dimension: Mass-Spectrometry-Based Metabolomics, Enzyme Assays, and Imaging. Handbook of Molecular Microbial Ecology I, 675–682.

Reindl, W., Bowen, B. P., Balamotis, M. A., Green, J. E., & Northen, T. R. (2011). Multivariate analysis of a 3D mass spectral image for examining tissue heterogeneity. Integrative Biology3(4), 460.

Northen, T. R. (2011). Biofuels and biomaterials from microbes. In D. S. Ginley & D. Kahen (Eds.), Fundamentals of Materials for Energy and Environmental Sustainability (p. 315). Cambridge University Press.


Wilmes, P., Bowen, B. P., Thomas, B. C., Mueller, R. S., Denef, V. J., VerBerkmoes, N. C., Hettich, R. L., Northen, T. R., & Banfield, J. F. (2010). Metabolome-Proteome Differentiation Coupled to Microbial Divergence. MBio1(5).

Baran, R., Bowen, B. P., Bouskill, N. J., Brodie, E. L., Yannone, S. M., & Northen, T. R. (2010). Metabolite Identification in Synechococcus sp. PCC 7002 Using Untargeted Stable Isotope Assisted Metabolite Profiling. Analytical Chemistry82(21), 9034–9042.

Bowen, B. P., & Northen, T. R. (2010). Dealing with the unknown: Metabolomics and Metabolite Atlases. Journal of the American Society for Mass Spectrometry21(9), 1471–1476.

Lee, D. Y., Bowen, B. P., & Northen, T. R. (2010). Mass spectrometry—based metabolomics, analysis of metabolite-protein interactions, and imaging. BioTechniques49(2), 557–565.

Jansson, C., & Northen, T. (2010). Calcifying cyanobacteria—the potential of biomineralization for carbon capture and storage. Current Opinion in Biotechnology21(3), 365–371.

Facciotti, M. T., Pang, W. L., Lo, F. Y., Whitehead, K., Koide, T., Masumura, K. I., Pan, M., Kaur, A., Larsen, D. J., Reiss, D. J., Hoang, L., Kalisiak, E., Northen, T., Trauger, S. A., Siuzdak, G., & Baliga, N. S. (2010). Large scale physiological readjustment during growth enables rapid, comprehensive and inexpensive systems analysis. BMC Systems Biology4(1).

Reindl, W., & Northen, T. R. (2010). Rapid Screening of Fatty Acids Using Nanostructure-Initiator Mass Spectrometry. Analytical Chemistry82(9), 3751–3755.

Baran, R., Reindl, W., & Northen, T. R. (2009). Mass spectrometry based metabolomics and enzymatic assays for functional genomics. Current Opinion in Microbiology12(5), 547–552.


Woo, H. K., Go, E. P., Hoang, L., Trauger, S. A., Bowen, B., Siuzdak, G., & Northen, T. R. (2009). Phosphonium labeling for increasing metabolomic coverage of neutral lipids using electrospray ionization mass spectrometry. Rapid Communications in Mass Spectrometry23(12), 1849–1855.

Yanes, O., Woo, H. K., Northen, T. R., Oppenheimer, S. R., Shriver, L., Apon, J., Estrada, M. N., Potchoiba, M. J., Steenwyk, R., Manchester, M., & Siuzdak, G. (2009). Nanostructure Initiator Mass Spectrometry: Tissue Imaging and Direct Biofluid Analysis. Analytical Chemistry81(8), 2969–2975.


Northen, T. R., Greving, M. P., & Woodbury, N. W. (2008). Combinatorial Screening of Biomimetic Protein Affinity Materials. Advanced Materials20(24), 4691–4697.

Woo, H. K., Northen, T. R., Yanes, O., & Siuzdak, G. (2008). Nanostructure-initiator mass spectrometry: a protocol for preparing and applying NIMS surfaces for high-sensitivity mass analysis. Nature Protocols, 3(8), 1341–1349.

Nordström, A., Want, E., Northen, T., Lehtiö, J., & Siuzdak, G. (2007). Multiple Ionization Mass Spectrometry Strategy Used To Reveal the Complexity of Metabolomics. Analytical Chemistry80(2), 421–429.